Skip to end of metadata
Go to start of metadata
Participants
Discussion topics
Item | Notes |
|---|
General updates | |
Individual updates | SB Mainly working on debugging issues with FE calcs using a different functional form. The custom nonbonded force we’re working on has a default softcore functionality. So you shouldn’t need to modify it to do FE calcs. But it turns out that the soft core potential insde the potential is more like a hard core in terms of the problems that come up. So I’m working with JHorton to figure out workarounds. JW – What’s the distinction between the X-core func forms? SB – I use it to mean “when you’re turning off interactions, and molecules need to semi-overlap, the LJ terms need to go to a very small number smoothly”. If you don’t satisfy this well, you end up getting poor sampling of certain states. It’s possible that modifying some global parameters could help here too, so we’re still looking into it. JS – Double expoential form: Is that similar to buckingham potential? SB – I think so - In buckingham you replace the r^12 term with an exponential. So here we’re experimenting with replacing both r^12 and r^6. By replacing r^6 we get nicer behavior at short range.
PB – When you have time, could you check the PR on plotmol?
Building training sets for refitting charge models - I’m putting together a set of molecules that we can compute electrostatic potentials for - Talked about how to put this together last week, decided that we’ll generate conformers and optimize offline, then submit to QCF to generate and store the wavefunctions online. I uploaded a tool called splore to conda for investigating molecule datasets
CC Made a new version of the dipeptide torsiondrive set. Goal was to expand number of sidechains. There’s one torsiondrive running for all 20 amino acids, and 6 protonation states. Saw one comment by PB about renaming one file from that PR, otehr than that it should eb good to go Will start playing around with fits in forcebalance. Will plan to mimic the terms in amber FF14SB initially. SB – More details? As in functional forms, or parameter smirks? CC – The fitting model - We want to fit terms for phi and psi, but we don’t know whether those should be shared between similar amino acids. SB – That makes sense. So this would start with the null model and see whether groupings provide an advantage? CC – Yes.
Starting to work on deeper review of paper, provide first round of feedback. Talked a few weeks ago about deriving charges for ELF10 - OE COOH issue. Is this still in progress? JW – I assigned this to JMitchell but he’s been offline for a few weeks. CC – I’d use this for deriving AM1BCC charges for making the protein librarycharges. This will become blocking in a ~month. SB – OE may have fixed this internally ina recent release? Alternatively, CBayly should have code for a workaround for this somewhere in the issue tracker.
MT General update - NEP29 recommended moving projects to Python 3.8+ on Dec 26 2021. I’ve updated my packages, but if anyone needs 3.7 support I may be able to support it but you’ll need to tell me. Was getting back into the swing of things last week. Tried to fix an entry points/plugin thing that JChodera pointed out, once that’s resolved we can release OFFTK 0.10.2. New interchange release will come with OFFTK 0.10.2 Been working on improving speed for export to large files. Won’t aim to be as fast as ParmEd initially, but working on reducing the time to write a gro file down from 10 minutes to something reasonable. Started identifying which packages will need to be updated for 0.11.0 release w/ topology refactor. We’ll be opening a bunch of PRs once the release candidate toolkit package is available.
DD QCArchive Pavan has the conn for qca-dataset-submission; he is the captain for submission lifecycle, priority, compute tag routing we had some headaches from SPICE calculations requiring high memory, high disk getting dipeptide set from Chapin submitted today; will spin up substantial resources on PRP for this identified with Ben a reasonable approach for fixing QCFractal manager signal handling; aiming to get PRs ready for review this week working with Ben this week to test out production-level calculations on managers against refactored QCFractal server
PLBenchmarks
JS PB JW – I’ll be out for jury duty tomorrow Continuing to work on topology refactor - getting rdkit specific code replicated by OE and into appropriate classes ensuring that residue data goes to/from openmm/rdkit/OE in a sane, documented way Turning from_pdb into a "one stop shop" that can handle a mix of small molecules and biopolymers Making errors more informative to help users with debugging
Updating roadmap items to each have at least a primary driver and primary stakeholder/approver, and for items that are already in progress, some form of a spec for what the minimum product is and what stage are anticipated in its development The preferred python plugin/entry point system recently had a small change, but adjusting to the new system required the redesign of our tests for parameterhandler plugins (OFFTK #1163). This is the last blocker to the 0.10.2 release Discussing requirements for 0.11.0 and how to incorporate Interchange. Big discussion on thread in #developers.
|
Action items
Decisions
Add Comment